Characterization of the low temperature properties of a simplified protein model

Prompted by results that showed that a simple protein model, the frustrated G\=o model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature properties of proteins. First, we examine equilibrium fluctuations. We calculate its incoherent neutron-scattering structure factor and show that it can be well described by a theory using the one-phonon approximation. By performing an inherent structure analysis, we assess the transitions among energy states at low temperatures. Then, we examine non-equilibrium fluctuations after a sudden cooling of the protein. We investigate the violation of the fluctuation--dissipation theorem in order to analyze the protein glass transition. We find that the effective temperature of the quenched protein deviates from the temperature of the thermostat, however it relaxes towards the actual temperature with an Arrhenius behavior as the waiting time increases. These results of the equilibrium and non-equilibrium studies converge to the conclusion that the apparent dynamical transition of this coarse-grained model cannot be attributed to a glassy behavior

Critical examination of the inherent-structure-landscape analysis of two-state folding proteins

Recent studies attracted the attention on the inherent structure landscape (ISL) approach as a reduced description of proteins allowing to map their full thermodynamic properties. However, the analysis has been so far limited to a single topology of a two-state folding protein, and the simplifying assumptions of the method have not been examined. In this work, we construct the thermodynamics of four two-state folding proteins of different sizes and secondary structure by MD simulations using the ISL method, and critically examine possible limitations of the method. Our results show that the ISL approach correctly describes the thermodynamics function, such as the specific heat, on a qualitative level. Using both analytical and numerical methods, we show that some quantitative limitations cannot be overcome with enhanced sampling or the inclusion of harmonic corrections.Comment: published Physical Review E, vol. 80, 061907-1-11 (2009

On 4-point correlation functions in simple polymer models

We derive an exact formula for the covariance of cartesian distances in two simple polymer models, the freely-jointed chain and a discrete flexible model with nearest-neighbor interaction. We show that even in the interaction-free case correlations exist as long as the two distances at least partially share the same segments. For the interacting case, we demonstrate that the naive expectation of increasing correlations with increasing interaction strength only holds in a finite range of values. Some suggestions for future single-molecule experiments are made

Can one predict DNA Transcription Start Sites by studying bubbles?

It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom which makes an accurate calculation difficult even for minimal models. In this letter, we introduce a new method that is orders of magnitude faster than MD. Using this method we show that the present evidence is unsubstantiated.Comment: 4 pages, 3 figures, accepted for publication in physical review letter

Goal conflict in chronic pain : day reconstruction method

Background When suffering from chronic pain, attempts to control or avoid pain often compete with other daily activities. Engaging in one activity excludes engaging in another, equally valued activity, which is referred to as “goal conflict.” As yet, the presence and effects of goal conflicts in patients with chronic pain remain poorly understood. Methods This study systematically mapped the presence and experience of goal conflicts in patients with fibromyalgia compared to healthy controls. A total of 40 patients and 37 controls completed a semi-structured interview in which they first reconstructed the previous day, identified conflicts experienced during that day, and classified each of the conflicting goals in one of nine goal categories. Additionally, they assessed how they experienced the previous day and the reported conflicts. Results Results showed that patients did not experience more goal conflicts than healthy controls, but that they did differ in the type of conflicts experienced. Compared to controls, patients reported more conflicts related to pain, and fewer conflicts involving work-related, social or pleasure-related goals. Moreover, patients experienced conflicts as more aversive and more difficult to resolve than control participants. Discussion This study provides more insight in the dynamics of goal conflict in daily life, and indicates that patients experience conflict as more aversive than controls, and that conflict between pain control (and avoidance) and other valued activities is part of the life of patients

Comment on "A generalized Langevin formalism of complete DNA melting transition"

We show that the calculated DNA denaturation curves for finite (Peyrard-Bishop-Dauxois (PBD) chains are intrinsically undefined.Comment: 2 pages. Accepted for EP

The result of acute induced psychosocial stress on pain sensitivity and modulation in healthy people

Background: Pain can be influenced by several factors, including stress. Stress can have various reactions on pain. These reactions are influenced by several internal factors such as gender, age, and experience with stress or pain. Objectives: To determine the effect of acute stress on mechanical hyperalgesia (with pressure pain thresholds [PPT]), endogenous pain facilitation (measured by temporal summation [TS]), and inhibition (measured by conditioned pain modulation [CPM]) in healthy people and to determine which factors are responsible for this stress result. Study Design: Pre-posttest design. Setting: Healthy volunteers from Belgium. Methods: One hundred and one healthy pain-free patients underwent a modified Trier Social Stress Test. Prior and following the stress manipulation, PPT, TS, and CPM efficacy were determined in the mm. trapezius and quadriceps and overall. Furthermore, possible explanatory factors, such as fear of pain, pain catastrophizing, pain hypervigilance, and daily activity levels, were assessed using questionnaires. Results: We found a significant stress result on widespread pain sensitivity, with an increase of PPT (P 0.05), and a decrease in CPM efficacy (P < 0.001). Factors associated with the stress result were age, previous surgery, attentional focus on the conditioning stimulus during CPM, fear of pain, and daily activity levels. Limitations: The efficacy of the stress manipulation was not examined, and the lack of a control group prevented to examine a real stress-effect. Furthermore, no physiologic parameters were measured as possibly influencing internal factors for the stress-result. Conclusions: The increase in PPT was not a clinically significant change, whereas the decrease in CPM was meaningful. None of the factors predicted the stress result in all experimental pain measurements, and the predictions that were observed only explained a small proportion of the observed effects

A Path to a Sustainable Trawl Fishery in Southeast Asia

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